I am using Adobe Illustrator 11.0.0 (MacBook Pro, OS 10.6.3) to lay out a sheet that shows a painting with calligraphy on top. The painting was photographed and saved as Photoshop RGB; the calligraphy is a scan of black ink calligraphy on white paper, with the white background erased to be transparent and saved as Photoshop graytone. The painting was saved as a JPEG, the calligraphy was saved as a PSD file.

The layout is fine. The black calligraphy lays on top of the colored painting. The strange thing is, in the thumbnail of the AI file (as seen in the Finder), the calligraphy shows up as white, not black. And, when I save the AI file as a PDF, the calligraphy also turns from black to white.